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trinity website  

Trinity contains three applications - Inchworm, Chrysalis, and Butterfly.

Using application with environment modules system

To use trinity with the environment modules system at HPC the following commands are available:

Get module information for trinity:

$module spider trinity

Load the default application module:

$module load trinity

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_TRINITY_DIR - directory where trinity is located.

How To Run

To run Trinity after you load the module use the "" perl script, or shell script, which is particularly useful as the optional ALLPATHS-LG software is enabled at UF HPC.

If the run produces an error that states that java could not create a virtual machine due to insufficient heap memory you can set the java memory with an

export _JAVA_OPTIONS="-Xmx2g"

command either at the command line if doing an interactive run on a test node or in the job script. Make sure that the value in the "-Xmx" is less then the amount of memory you requested from the batch system.